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  • CellKb Immune: a manually curated database of mammalian hematopoietic marker gene sets for rapid cell type identification.
    Ajay Patil & Ashwini Patil, bioRxiv 2020.12.01.389890, 2020. [Article]
Publications citing CellKb (34)
2025 (7)
  • Targeting the poliovirus receptor to activate T cells and induce myeloid-derived suppressor cells to differentiate to pro-inflammatory macrophages via the IFN-γ-p-STAT1-IRF8 axis in cancer therapy.
    Feng, M., Ma, Q., Zhang, B. et al. Cell Death Differ. (2025). [Article]
  • Retinoic acid antagonizes estrogen signaling to maintain adult uterine cell fate.
    Yin Y, Haller M, Goldinger L, Bharadwaj S, So E, Robles-Pinos V, Chen D, Ma L. Proc Natl Acad Sci USA., 2025 Feb 4;122(5):e2416089122. [Article]
  • iPSCs engrafted in allogeneic hosts without immunosuppression induce donor-specific tolerance to secondary allografts.
    Kamatani T, Kimura R, Ikeda S, Inoue M, Seino KI. Proc Natl Acad Sci USA., 2025 Mar 18;122(11):e2413398122. [Article]
  • Mapping the transcriptional and epigenetic landscape of organotypic endothelial diversity in the developing and adult mouse.
    Cantu Gutierrez ME, Hill MC, Largoza GE, Gillespie WB 3rd, Martin JF, Wythe JD. Nature Cariovascular Research., 2025 Mar 17. [Article]
  • Immunogenic shift of arginine metabolism triggers systemic metabolic and immunological reprogramming to suppress HER2+ breast cancer.
    Sharma V, Fernando V, Zheng X, Choi ES, Sweef O, Thomas V, Szpendyk J, Furuta S. Cancer Metab. , 2025 Mar 20;13(1):15.. [Article]
  • CXCL10 Promotes Spinal Macrophage Recruitment via the JAK/STAT3 Pathway to Induce Pain in Experimental Autoimmune Prostatitis.
    Chen L, Chen Z, Chen J, Du H, Chen X, Chen J, Wang H, Liang C. Cell Proliferation, 2025 Apr;58(4);e13784. [Article]
  • The mitochondrial NAD transporter SLC25A51 is a modulator of beta cell senescence and type 2 diabetes.
    Byungsoo Kong, Sehi L'Yi, Erika Gabriela Ramirez-Hernandez, Serin Hong, Rosa Weidenspointner, Suyeon Song, Chase Caserta, Young Min Cho, Nora Kory. bioRxiv, bioRxiv 2025.04.09.647991; [Article]
2024 (9)
  • PD-L1 protects tumor-associated dendritic cells from ferroptosis during immunogenic chemotherapy.
    Kaimin Xiao, Silin Zhang, Qi Peng, Yuxia Du, Xiyue Yao, Ian-Ian Ng, Haidong Tang. Cell Reports, 2024 Nov 26;43(11):114868. [Article]
  • A pairwise cytokine code explains the organism-wide response to sepsis.
    Michihiro Takahama, Ashwini Patil, Gabriella Richey, Denis Cipurko, Katherine Johnson, Peter Carbonetto, Madison Plaster, Surya Pandey, Katerina Cheronis, Tatsuki Ueda, Adam Gruenbaum, Tadafumi Kawamoto, Matthew Stephens & Nicolas Chevrier. Nature Immunology, 25:226, 2024. [Article]
  • Heterogeneous stiffness of the bone marrow microenvironment regulates the fate decision of haematopoietic stem and progenitor cells.
    Guolin Shi, Zhuo Chang, Pan Zhang, Xiaohang Zou, Xinmin Zheng, Xiru Liu, Jinxiao Yan, Huiyun Xu, Zhenhao Tian, Nu Zhang, Ning Cui, Leming Sun, Guangkui Xu, Hui Yang. Cell Proliferation in basic and clinical sciences, DOI: 10.1111/cpr.13715, 2024. [Article]
  • Single-cell view into the role of microbiota shaping host immunity in the larynx.
    Ran An, Zijian Ni, Elliott Xie, Federico E. Rey, Christina Kendziorski, Susan L.Thibeault. iScience, 27(6):110156, 2024. [Article]
  • Glomerular-tubular crosstalk via cold shock Y-box binding protein-1 in the kidney.
    Rajiv Rana, Jayakumar Manoharan, Ahmed Elwakiel, Silke Zimmermann, Jonathan A. Lindquist, Dheerendra Gupta, Moh'd Mohanad Al-Dabet, Ihsan Gadi, Jörg Fallmann, Kunal Singh, Anubhuti Gupta, Ronald Biemann, Sabine Brandt, Bekas Alo, Paul Kluge, Ravindra Garde, Christina Lamers, Khurrum Shahzad, Georg Künze, Shrey Kohli, Peter R. Mertens & Berend Isermann. Kidney International, 105(1):65, 2024. [Article]
  • Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer.
    Anna Vyhlídalová Kotrbová, Kristína Gömöryová, Antónia Mikulová, Hana Plešingerová, Stanislava Sladeček, Marek Kravec, Šárka Hrachovinová, David Potěšil, Garett Dunsmore, Camille Blériot, Mathilde Bied, Jan Kotouček, Markéta Bednaříková, Jitka Hausnerová, Luboš Minář, Igor Crha, Michal Felsinger, Zbyněk Zdráhal, Florent Ginhoux, Vít Weinberger, Vitězslav Bryja, Vendula Pospíchalová. Journal of Extracellular Vesicles, 13(3):e12420, 2024. [Article]
  • THBS1+ myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1.
    Julie Giraud, Domitille Chalopin, Eloise Ramel,Thomas Boyer,Atika Zouine,Marie-Alix Derieppe,Nicolas Larmonier, Olivier Adotevi,Brigitte Le Bail, Jean-Frederic Blanc, Christophe Laurent, Laurence Chiche, Marc Derive, Macha Nikolski & Maya Saleh. Cell Reports, 43(2):113773, 2024. [Article]
  • A mouse model of Zhu-Tokita-Takenouchi-Kim syndrome reveals indispensable SON functions in organ development and hematopoiesis.
    Vukadin L, Park B, Mohamed M, Li H, Elkholy A, Torrelli-Diljohn A, Kim JH, Jeong K, Murphy JM, Harvey CA, Dunlap S, Gehrs L, Lee H, Kim HG, Sah JP, Lee SN, Stanford D, Barrington RA, Foote JB, Sorace AG, Welner RS, Hildreth BE 3rd, Lim SS, Ahn EE. JCI Insight, 2024 Mar 8;9(5):e175053. [Article]
  • Clonal spheroids capture functional and genetic heterogeneity of head and neck cancer.
    Jyoti Pandey, Md. Zubbair Malik, Ritis K Shyanti, Palak Parashar, Praveen K Kujur, Deepali Mishra, Dhanir Tailor, Jee Min Lee, Tejinder Kataria, Deepak Gupta, Hitesh Verma, Sanjay V Malhotra, Suneel Kateriya, Vibha Tandon, Rupesh Chaturvedi, Rana P Singh. bioRxiv, 2024.05.24.595655, 2024. [Article]
2023 (11)
  • Prenatal exposure to bisphenol AF induced male offspring reproductive dysfunction by triggering testicular innate and adaptive immune responses.
    Senlin Xue, Lianqin Liu, Mengmeng Dong, Wei Xue, Shenrui Zhou, Xiaotian Li, Sihui Guo, Wei Yan. Ecotoxicology and Environmental Safety, 259:115030, 2023. [Article]
  • A CSF-1R-blocking antibody/IL-10 fusion protein increases anti-tumor immunity by effectuating tumor-resident CD8+ T cells.
    Yao-Wen Chang, Huey-Wen Hsiao, Ju-Pei Chen, Sheue-Fen Tzeng, Chin-Hsien Tsai, Chun-Yi Wu, Hsin-Hua Hsieh, Santiago J. Carmona, Massimo Andreatta, Giusy Di Conza, Mei-Tzu Su, Pandelakis A. Koni, Ping-Chih Ho, Hung-Kai Chen, Muh-Hwa Yang. Cell Reports Medicine, 4(8):101154, 2023. [Article]
  • Investigating how glioblastoma tumor cells exploit their metabolic microenvironment.
    Chloe Shard, Rebecca Ormsby, Santosh Poonnoose, John Toubia, Paul Trim, Lisa Ebert, Ashwini Patil & Guillermo Gomez. Neuro-Oncology, 25(Supplement_5):v274, 2023. [Article]
  • Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice.
    Adriana Vasquez Ayala, Chia-Yun Hsu, Renee E. Oles, Kazuhiko Matsuo, Luke R. Loomis, Ekaterina Buzun, Marvic Carrillo Terrazas, Romana R. Gerner, Hsueh-Han Lu, Sohee Kim, Ziyue Zhang, Jong Hwee Park, Paul Rivaud, Matt Thomson, Li-Fan Lu, Booki Min, Hiutung Chu. Journal of Experimental Medicine, 221(1):e20230063, 2023. [Article]
  • Glycolytic shift during West Nile virus infection provides new therapeutic opportunities.
    Patricia Mingo-Casas, Ana-Belén Blázquez, Marta Gómez de Cedrón, Ana San-Félix, Susana Molina, Estela Escribano-Romero, Eva Calvo-Pinilla, Nereida Jiménez de Oya, Ana Ramírez de Molina, Juan-Carlos Saiz, María-Jesús Pérez-Pérez & Miguel A. Martín-Acebes. Journal of Neuroinflammation, 20:217, 2023. [Article]
  • Integrated multi-omics analysis reveals insights into Chinese forest musk deer (Moschus berezovskii) genome evolution and musk synthesis.
    Feng H, Feng T, Mo Y, Sun S, Wang L, Lu C, Feng C, Xing K & Su Z. Frontiers in Cell and Development Biology, 11:1156138, 2023. [Article]
  • Metformin suppresses calcium oxalate crystal-induced kidney injury by promoting Sirt1 and M2 macrophage-mediated anti-inflammatory activation.
    Haoran Liu, Chen Duan, Xiaoqi Yang, Jianhe Liu, Yaoliang Deng, Hans-Göran Tiselius, Zhangqun Ye, Tao Wang, Jinchun Xing & Hua Xu. Signal Transduction and Targeted Therapy, 8(1):38, 2023. [Article]
  • Tumor Microenvironment and Genes Affecting the Prognosis of Temozolomide-Treated Glioblastoma.
    Jang Y, Cheong W, Park G, Kim Y, Ha J & Ahn S. Journal of Personalized Medicine, 13(2):188, 2023. [Article]
  • Determinants of renin cell differentiation: a single cell epi-transcriptomics approach.
    Alexandre G Martini, Jason P. Smith, Silvia Medrano, Nathan C. Sheffield, Maria Luisa S. Sequeira-Lopez & R. Ariel Gomez. bioRxiv 2023.01.18.524595, 2023. [Article]
  • CIA: a Cluster Independent Annotation method to investigate cell identities in scRNA-seq data.
    Ivan Ferrari, Mattia Battistella, Francesca Vincenti, Andrea Gobbini, Samuele Notarbartolo, Jole Costanza, Stefano Biffo, Renata Grifantini, Sergio Abrignani, Eugenia Galeota. bioRxiv 2023.11.30.569382. [Article]
  • Publication, Funding, and Experimental Data in Support of Human Reference Atlas Construction and Usage.
    Yongxin Kong & Katy Börner. bioRxiv 2023.10.21.563417, 2023. [Article]
2022 (4)
  • Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
    Christa Haase, Karin Gustafsson, Shenglin Mei, Shu-Chi Yeh, Dmitry Richter, Jelena Milosevic, Raphaël Turcotte, Peter V. Kharchenko, David B. Sykes, David T. Scadden & Charles P. Lin. Nature Methods, 19(12):1622, 2022. [Article]
  • WebCSEA: web-based cell-type-specific enrichment analysis of genes.
    Yulin Dai, Ruifeng Hu, Andi Liu, Kyung Serk Cho, Astrid Marilyn Manuel, Xiaoyang Li, Xianjun Dong, Peilin Jia & Zhongming Zhao. Nucleic Acids Research, 50(W1):W782, 2022. [Article]
  • Tetrabromobisphenol A effects on differentiating mouse embryonic stem cells reveals unexpected impact on immune system.
    Tribondeau Alicia, Sachs Laurent M & Buisine Nicolas. Frontiers in Genetics, 13:996826, 2022. [Article]
  • Tumor-associated macrophages are shaped by intratumoral high potassium via Kir2.1
    Sheng Chen, Wenyu Cui, Zhexu Chi, Qian Xiao, Tianyi Hu, Qizhen Ye, Kaixiang Zhu, Weiwei Yu, Zhen Wang, Chenxuan Yu, Xiang Pan, Siqi Dai, Qi Yang, Jiacheng Jin, Jian Zhang, Mobai Li, Dehang Yang, Qianzhou Yu, Quanquan Wang, Xiafei Yu, Wei Yang, Xue Zhang, Junbin Qian, Kefeng Ding & Di Wang. Cell Metabolism, 34(11):1843, 2022. [Article]
2021 (2)
  • Hypoxia‐inducible factor‐dependent induction of myeloid‐derived netrin‐1 attenuates natural killer cell infiltration during endotoxin‐induced lung injury.
    Nathaniel K Berg, Jiwen Li, Boyun Kim, Tingting Mills, Guangsheng Pei, Zhongming Zhao, Xiangyun Li, Xu Zhang, Wei Ruan, Holger K Eltzschig, Xiaoyi Yuan. FASEB J, 35(4):e21334, 2021. [Article]
  • A deep convolutional neural network for segmentation of whole-slide pathology images identifies novel tumour cell-perivascular niche interactions that are associated with poor survival in glioblastoma.
    Amin Zadeh Shirazi, Mark D. McDonnell, Eric Fornaciari, Narjes Sadat Bagherian, Kaitlin G. Scheer, Michael S. Samuel, Mahdi Yaghoobi, Rebecca J. Ormsby, Santosh Poonnoose, Damon J. Tumes & Guillermo A. Gomez. British Journal of Cancer, 125(3):337, 2021. [Article]
2020 (1)
  • Unsupervised Identification of SARS-CoV-2 Target Cell Groups via Nonlinear Dimensionality Reduction on Single-cell RNA-Seq Data.
    Saiteja Danda, Akram Vasighizaker & Luis Rueda. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020. [Article]